FragmentEquivalentClassNormalization: The FragmentEquivalentClassNormalization class
In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

FragmentEquivalentClassNormalization

R Documentation

The FragmentEquivalentClassNormalization class

Description

Package: aroma.affymetrix
Class FragmentEquivalentClassNormalization

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--ChipEffectTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--FragmentEquivalentClassNormalization

Directly known subclasses:

public static class FragmentEquivalentClassNormalization
extends ChipEffectTransform

This class represents a normalization method that corrects for systematic effects between loci of different equivalent classes of pairs of sequences that are recognized by the restriction enzymes that cut the DNA studies.

Usage

FragmentEquivalentClassNormalization(dataSet=NULL, ..., targetAvgs=NULL,
  subsetToFit="-XY")

Arguments

`dataSet`	A `CnChipEffectSet`.
`...`	Additional arguments passed to the constructor of `ChipEffectTransform`.
`targetAvgs`	An optional list of `function`s. For each enzyme there is one target averages to which all arrays should be normalized to.
`subsetToFit`	The units from which the normalization curve should be estimated. If `NULL`, all are considered.

Fields and Methods

Methods:

	`getAromaUfcFile`	-
	`getCdf`	-
	`process`	-

Methods inherited from ChipEffectTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis

Requirements

This class requires an UFC (Unit Fragment Class) annotation file.

Acknowledgments

The idea of normalization signals stratified on enzyme recognition sequences is credited to Jim Veitch and Ben Bolstad at Affymetrix Inc. (2008) who have designed a similar method for copy number estimation in the Affymetrix' Genotype Console v2.